Cone beam computed tomography (CBCT) used in dental medicine results in complex dose distributions owing to different performance of devices and examination procedures. Consensus within scientific and professional community regarding dosimetric quantity has not been reached yet and conversion factors by which effective dose of the patient could be estimated are not given. The aim of this study is to examine the appropriateness of the suggested dose indices (CT dose index, CBCT dose indices and dose-area product (DAP)) and to show their advantages and disadvantages as well as to examine the influence of scanning parameters defining the CBCT procedure to dose indices, organ doses and effective dose of the patient. Investigation was performed by the use of Monte Carlo simulation and experimental measurements. CBCT dental unit was simulated using Monte Carlo N-Particle transport code (MCNP® 6.1.1beta). For the model verification purposes, PMMA head CTDI phantom and radiochromic films were used. For calculation of organ doses and for the assessment of effective doses computational anthropomorphic phantom was used („Zubal“). Most often clinical protocols involving different exposure geometries including sizes and positions of fields of view (FOV), 180o and 360o X-ray tube rotation angles, different tube current-exposure time products (mAs) and photon energies were simulated. Measured (CTDI and DAP) and simulated dose indices (CBCT dose indices) were compared to effective doses for every exposure geometry and analysed.Organ doses in all simulated CBCT protocols ranged from 35 μGy (brain) to 4119 μGy (bone surface) and effective doses from 22 μSv to 218 μSv, depending on scanning parameters. In average, thyroid gland has the highest contribution to the effective dose (31%) followed by salivary glands (25 %) and extra thoracic region (21%). Results of this study indicate importance of careful choice of FOV's size and its position in optimisation of CBCT procedures considering clinical question and anthropometric features of the patient since size and position of FOV have great impact on organ doses and effective dose, especially on thyroid gland and salivary glands. Choosing 180o for the X-ray tube rotation angle instead of 360o would not decrease image quality but may significantly decrease doses of the organs contributing the most to the effective dose. Due to linear dependence of organ doses and effective dose on mAs, whenever possible lowest mAs should be used, considering level of the image quality required. According to the results of this study, change of tube voltage by ±10 kV does not result in significant change neither of organ doses nor effective dose so further investigation employing greater range of tube potentials while considering image quality is needed. Although DAP introduces a large uncertainty in the risk measure in dental CBCT, after thorough investigation of the relationship of the effective dose and aforementioned dose indices, it is suggested as the most appropriate dose index for the optimisation purposes and estimation of effective dose of the patient since it represents the dose and FOV which are the most important scanning parameters affecting the dose. To decrease uncertainty on the risk measure, the effective dose has to be estimated for FOV position and sizes, considering both, tube rotation angle and tube voltage.